---
vault_clearance: EUCLID
halo:
  classification: INTERNAL
  confidence: HIGH
  front: "22_Project_StarSight"
  custodian: "The Architect"
  created: 2026-03-30
  updated: 2026-03-31
  wing: CONDITIONAL
  containment: "Bioimaging vision stack map — references RESTRICTED wet-lab paths by pointer only"
---

# 22_Project_StarSight

**StarSight** is the lab’s **orthodox composite grandmaster** for **biological and microscopy image analysis**: a single place to stack the field’s conventional tooling (max parameters, max integrations) against a **minimal rogue lane** (deterministic QC, human verification, vault scripts). It does **not** claim Cook–Levin NP-completeness; “NP-complete orthodox cultivator” here means the **strongest max-traditional suite you can name and wire**, built to be beaten—see [FORM_PROTOCOL.md](../FORM_PROTOCOL.md) §5.

**Start here:** [FORM.md](FORM.md) (paradigm + tier ladder) · [BOOK.md](BOOK.md) (citations, software registry, benchmarks) · [BOUNTY_BOARD.md](BOUNTY_BOARD.md) · [WORLDLINE.md](WORLDLINE.md)

**Vault spine:** [Lab protocol](../README.md#lab-protocol) · [Vault board](../BOUNTY_BOARD.md) · [Vault worldline](../WORLDLINE.md)

---

## What this project owns

| Surface | Role |
|---------|------|
| **FORM.md** | Orthodox apex imaging pipeline vs rogue lane; failure modes; proof ladder for vision claims |
| **BOOK.md** | DOIs, tool URLs, public benchmarks, open formats — arms the FORM |

**Out of scope for this folder:** raw image bytes. Exemplar **RESTRICTED** wet-lab material lives under **10** (see [BOOK_Protocol.md](../BOOK_Protocol.md) wet-lab USB ingest; [HALO_PROTOCOL.md](../HALO_PROTOCOL.md)). StarSight only **points** at those paths.

---

## Run the Vision Dao Monarch (vault runner)

**Integrated Python toolset (default):** Pillow + **tifffile** metadata, numpy thumbnails, scipy (watershed distance transform), scikit-image (**Canny**, **entropy/Haralick/blobs**, **TV denoise probe**, **Otsu+watershed** counts), OpenCV (**ORB**, **SIFT**, **phase correlation + Farneback** on the first image pair), optional matplotlib histogram (`--with-figures`). Writes **VDM_REPORT.md** + **vdm-report.json** with a full tier trace. **Fiji / QuPath / CellProfiler / Bio-Formats GUI / stitching / tracking** are not subprocess-invoked — the report lists what remains external.

1. `pip install -r 22_Project_StarSight/requirements-runner.txt` (see file for scipy, tifffile, imageio, OpenCV, skimage, matplotlib).
2. From vault root: `python scripts/vision_dao_monarch_run.py --input path/to/your/images` (add `--with-figures` for `figures/luminance_hist.png`). **`--cell-morphology`** adds per-cell `skimage` regionprops on masks (Cellpose, StarDist, or classical watershed); **`--phenocluster-k K`** runs pooled `sklearn` MiniBatchKMeans (unsupervised screening, not biological labels). Use **`--fast`** to drop TV/Haralick/watershed/SIFT/pair registration. **`--input` is recursive** (`os.walk`); see `walk_recursive` in JSON.
3. Default report location when you omit `--output-dir`: `out/vdm_runs/<run_id>/VDM_REPORT.md`. For **publication-oriented** batches, use the integration script or `.bat` below so outputs land under **`outs/runs/`** inside this project.

**Deep segmentation (optional):** `pip install -r 22_Project_StarSight/requirements-runner-segmentation.txt` and `--segmentation cellpose`, or `pip install -r 22_Project_StarSight/requirements-runner-stardist.txt` and `--segmentation stardist`. Full ordered pip list: [requirements-runner-full.txt](requirements-runner-full.txt).

For the broader annotation vs no-label landscape (DOIs, lanes A–E, cell-type honesty), see [BOOK.md §6](BOOK.md#6-annotation-tooling-and-no-manual-label-paths-image--counts--analysis).

Details and flags: [FORM.md](FORM.md) section H4. Report schema: [templates/VISION_DAO_MONARCH_REPORT.template.md](templates/VISION_DAO_MONARCH_REPORT.template.md).

### Structured outputs (`outs/`) — publication and re-analysis

Canonical layout (this repo):

| Path | Role |
|------|------|
| [outs/README.md](outs/README.md) | Index of `runs/`, `publication/`, `LATEST_RUN.txt` |
| `outs/runs/imaging_<run_id>/` | Full VDM bundle from `starsight_pipeline_test.py --imaging` (default) |
| `outs/runs/cellpose_<run_id>/` | Optional Cellpose sample (`--cellpose`) |
| [outs/publication/](outs/publication/) | `LAST_RUN.json`, `RUN_LOG.md` — pointers for Methods / auditing |

**Integration script (vault root):** `python scripts/starsight_pipeline_test.py` (self-check only); `--imaging` (default cap **12** files); **`--imaging --all-images`** (entire tree, recursive); `--cellpose` (one image, slow). Input: `10_Project_DiscordIntoSymphony/data/imaging` or **`STARSIGHT_TEST_INPUT`**. Default output: **`22_Project_StarSight/outs/runs/...`**. **`--legacy-vault-out`**, **`--output-dir`** as before.

**Windows one-shot:** [StarSight_publication_run.bat](StarSight_publication_run.bat) (`pushd` to vault root, then imaging pass). **Default: every image** under the lab imaging folder (`--all-images`). Set **`STARSIGHT_MAX_FILES=24`** (or any N) before running for a capped smoke pass only. The window **stays open** at the end (double-click from Explorer). `STARSIGHT_RUN_CELLPOSE=1` adds Cellpose after imaging; `STARSIGHT_NO_PAUSE=1` exits immediately (automation).

### Docker EYE (EYE-14)

Reproducible **CPU** and **GPU** images: build/run commands, GPU notes, compose, troubleshooting — [docker/RUNBOOK.md](docker/RUNBOOK.md). Build context is the **vault root**; mount the vault at `/vault`. Writes can target **`/vault/22_Project_StarSight/outs/runs/...`** by passing `--output-dir` on the runner, or the default **`/vault/out/vdm_runs/<run_id>`** if you omit it. Registry: [EYE_PROTOCOL.md](../EYE_PROTOCOL.md) (EYE-14).

**Host-side quick verify (no container):** same as the integration script above; full detail was **fused** here so Docker runbook stays image-specific.

---

## Feeds and neighbors

| Project | Relationship |
|---------|----------------|
| **10 DiscordIntoSymphony** | Primary **in-vault** microscopy exemplars (`data/usb_ingest_*`); genomics context for the same biological program |
| **15 ShadowsOfSight** | Integrity / attestations when image artifacts or manifests must be sealed |
| **17 CerberusLantern** | When vision pipelines touch **verification** or hostile-disk posture |
| **16 Constellation** | Optional future **FORM_ORTHODOX_APEX_TOOLING** chapter for cited toolbars |

---

## Quick links

- [FORM_PROTOCOL.md](../FORM_PROTOCOL.md) — FORM–TRUTH axes; §5 max-orthodox map
- [BOOK_Protocol.md](../BOOK_Protocol.md) — BOOK convention + code/storage index
- [scripts/usb_ingest_image_profile.py](../scripts/usb_ingest_image_profile.py) — example deterministic QC over ingest JPEG/TIFF
- [scripts/vision_dao_monarch_run.py](../scripts/vision_dao_monarch_run.py) — Vision Dao Monarch runner (FORM §H4)
- [scripts/starsight_pipeline_test.py](../scripts/starsight_pipeline_test.py) — smoke; default writes under **`outs/runs/`** (see above)
- [StarSight_publication_run.bat](StarSight_publication_run.bat) — Windows bundle: self-check + imaging (+ optional Cellpose)